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High-resolution association mapping of number of teats in pigs reveals regions controlling vertebral development.

ABSTRACT: BACKGROUND: Selection pressure on the number of teats has been applied to be able to provide enough teats for the increase in litter size in pigs. Although many QTL were reported, they cover large chromosomal regions and the functional mutations and their underlying biological mechanisms have not yet been identified. To gain a better insight in the genetic architecture of the trait number of teats, we performed a genome-wide association study by genotyping 936 Large White pigs using the Illumina PorcineSNP60 Beadchip. The analysis is based on deregressed breeding values to account for the dense family structure and a Bayesian approach for estimation of the SNP effects. RESULTS: The genome-wide association study resulted in 212 significant SNPs. In total, 39 QTL regions were defined including 170 SNPs on 13 Sus scrofa chromosomes (SSC) of which 5 regions on SSC7, 9, 10, 12 and 14 were highly significant. All significantly associated regions together explain 9.5% of the genetic variance where a QTL on SSC7 explains the most genetic variance (2.5%). For the five highly significant QTL regions, a search for candidate genes was performed. The most convincing candidate genes were VRTN and Prox2 on SSC7, MPP7, ARMC4, and MKX on SSC10, and vertebrae ?-EF1 on SSC12. All three QTL contain candidate genes which are known to be associated with vertebral development. In the new QTL regions on SSC9 and SSC14, no obvious candidate genes were identified. CONCLUSIONS: Five major QTL were found at high resolution on SSC7, 9, 10, 12, and 14 of which the QTL on SSC9 and SSC14 are the first ones to be reported on these chromosomes. The significant SNPs found in this study could be used in selection to increase number of teats in pigs, so that the increasing number of live-born piglets can be nursed by the sow. This study points to common genetic mechanisms regulating number of vertebrae and number of teats.

SUBMITTER: Duijvesteijn N

PROVIDER: S-EPMC4092218 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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High-resolution association mapping of number of teats in pigs reveals regions controlling vertebral development.

Duijvesteijn Naomi N Veltmaat Jacqueline M JM Knol Egbert F EF Harlizius Barbara B

BMC genomics 20140630

<h4>Background</h4>Selection pressure on the number of teats has been applied to be able to provide enough teats for the increase in litter size in pigs. Although many QTL were reported, they cover large chromosomal regions and the functional mutations and their underlying biological mechanisms have not yet been identified. To gain a better insight in the genetic architecture of the trait number of teats, we performed a genome-wide association study by genotyping 936 Large White pigs using the I ...[more]

PMID: 24981054

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Project description:Modern breeding schemes for livestock species accumulate a large amount of genotype and phenotype data which can be used for genome-wide association studies (GWAS). Many chromosomal regions harboring effects on quantitative traits have been reported from these studies, but the underlying causative mutations remain mostly undetected. In this study, we combine large genotype and phenotype data available from a commercial pig breeding scheme for three different breeds (Duroc, Landrace, and Large White) to pinpoint functional variation for a region on porcine chromosome 7 affecting number of teats (NTE). Our results show that refining trait definition by counting number of vertebrae (NVE) and ribs (RIB) helps to reduce noise from other genetic variation and increases heritability from 0.28 up to 0.62 NVE and 0.78 RIB in Duroc. However, in Landrace, the effect of the same QTL on NTE mainly affects NVE and not RIB, which is reflected in reduced heritability for RIB (0.24) compared to NVE (0.59). Further, differences in allele frequencies and accuracy of rib counting influence genetic parameters. Correction for the top SNP does not detect any other QTL effect on NTE, NVE, or RIB in Landrace or Duroc. At the molecular level, haplotypes derived from 660K SNP data detects a core haplotype of seven SNPs in Duroc. Sequence analysis of 16 Duroc animals shows that two functional mutations of the Vertnin (VRTN) gene known to increase number of thoracic vertebrae (ribs) reside on this haplotype. In Landrace, the linkage disequilibrium (LD) extends over a region of more than 3 Mb also containing both VRTN mutations. Here, other modifying loci are expected to cause the breed-specific effect. Additional variants found on the wildtype haplotype surrounding the VRTN region in all sequenced Landrace animals point toward breed specific differences which are expected to be present also across the whole genome. This Landrace specific haplotype contains two missense mutations in the ABCD4 gene, one of which is expected to have a negative effect on the protein function. Together, the integration of largescale genotype, phenotype and sequence data shows exemplarily how population parameters are influenced by underlying variation at the molecular level.

Project description:BACKGROUND: The number of vertebrae in pigs varies and is associated with body size. Wild boars have 19 vertebrae, but European commercial breeds for pork production have 20 to 23 vertebrae. We previously identified two quantitative trait loci (QTLs) for number of vertebrae on Sus scrofa chromosomes (SSC) 1 and 7, and reported that an orphan nuclear receptor, NR6A1, was located at the QTL on SSC1. At the NR6A1 locus, wild boars and Asian local breed pigs had the wild-type allele and European commercial-breed pigs had an allele associated with increased numbers of vertebrae (number-increase allele). RESULTS: Here, we performed a map-based study to define the other QTL, on SSC7, for which we detected genetic diversity in European commercial breeds. Haplotype analysis with microsatellite markers revealed a 41-kb conserved region within all the number-increase alleles in the present study. We also developed single nucleotide polymorphisms (SNPs) in the 450-kb region around the QTL and used them for a linkage disequilibrium analysis and an association study in 199 independent animals. Three haplotype blocks were detected, and SNPs in the 41-kb region presented the highest associations with the number of vertebrae. This region encodes an uncharacterized hypothetical protein that is not a member of any other known gene family. Orthologs appear to exist not only in mammals but also birds and fish. This gene, which we have named vertnin (VRTN) is a candidate for the gene associated with variation in vertebral number. In pigs, the number-increase allele was expressed more abundantly than the wild-type allele in embryos. Among candidate polymorphisms, there is an insertion of a SINE element (PRE1) into the intron of the Q allele as well as the SNPs in the promoter region. CONCLUSIONS: Genetic diversity of VRTN is the suspected cause of the heterogeneity of the number of vertebrae in commercial-breed pigs, so the polymorphism information should be directly useful for assessing the genetic ability of individual animals. The number-increase allele of swine VRTN was suggested to add an additional thoracic segment to the animal. Functional analysis of VRTN may provide novel findings in the areas of developmental biology.

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High-resolution association mapping of number of teats in pigs reveals regions controlling vertebral development.

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High-resolution association mapping of number of teats in pigs reveals regions controlling vertebral development.

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